Catholic schools have been issued with a strong warning against becoming academies over fears the move will dilute faith-based education.
The Catholic Education Service (CES) has advised "great caution" in exploring academy status amid concerns it could rob schools of their Catholic ethos, weaken control over admissions and take away rights over land and buildings.
In guidance for schools, Oona Stannard, chief executive of the CES, said the extra money that comes with being an academy may seem attractive. However, the fact that Catholic schools currently contribute 10 per cent towards their capital costs "at present buys our sector a degree of valuable independence along the lines of 'he who pays the piper calls the tune'", Ms Stannard wrote.
"We would be very unwise to trade this for an uncertain future and a higher level of risk."
The Church of England is also advising its schools not to become academies in the first wave of the programme's expansion this September.
Both the CofE and the Catholic Church are concerned that local church dioceses could lose their power to appoint the majority of governors to voluntary-aided schools. This could weaken the link between the Church and schools and risks fragmenting their "families" of church schools, they said.
The Catholic guidance also raises concerns that a switch to academy status could put at risk the rights voluntary-aided faith schools have to dedicate 10 per cent of their curriculum to religious education and to devise their own sex and relationships education policies.
The Government has said all schools rated "outstanding" by Ofsted are pre-approved to become academies and that others will be able to apply later in the year.
Figures released earlier this month showed that more than 1,100 schools have already expressed interest in making the switch.
Reverend Jan Ainsworth, the CofE's chief education officer, said that between 150 and 200 CofE schools had approached their local diocese to express interest or find out more information.
"There is so much detail specific to voluntary-aided schools that has not been decided," she said. "There are also big questions about what happens if the majority of schools get academy status. What happens to the family of schools in a diocese when those links are severed? There are risks, but we are working to make sure they are minimised."
Revd Ainsworth said the CofE did not have a strong line on whether its schools should become academies, but advised against becoming involved until the details had been finalised.
"Academies were a way of returning to the Church's original purpose to provide good education in areas of need," Revd Ainsworth said. "This certainly dilutes that original motivation. We have questions about how that commitment to the poor and disadvantaged will be maintained."
Guidance put out by the Department for Education last week said voluntary-aided faith schools would need the permission of their diocese before they could become academies.
A DfE spokesman said existing admissions powers would be retained and that private land owned by voluntary-aided schools would not come under the control of the secretary of state.